This also happened to me with whole blood DNA extraction.....try to
eliminate sucrose from your buffer and increase EDTA at a concentration
of 100 mM...and if you still have problem to separate the phases check
you centrifuge your samples all at RT (25 degrees C) . If you still have
the problem try to dilute your samples by adding 1 more Volume of
buffer prior to centrifugation .
Hope this will help you !!!
PS
Firts of all CHECK TEMPERATURE OF CENTRIFUGATION THIS IS CRITYCAL FOR
PHASE SEPARATION !!!!!!
bye !